Ok, I understand what you mean. I used several gear calculators (math works a bit better for me to understand things), like the one you can find on the ParkTools site, and they all told me that my chain was put on one link too long. Taking it to the shop, the guys weren't crazy about removing the link, but it still seems safe in terms of not pulling the RD pulleys too taught. It's still not ideal such that I don't think I can run larger than a 25T cog on the rear with this bike. They said I just didn't luck out with the components I chose on this frame.
Anyway, I just wanted to point out that there can be some problems caused by erring on the side of a chain that is too long. Yes, it is can be catastrophic to have a chain that is definitely too short. I guess I am just advocating making sure the chain is properly sized for the individual setup.